Could you please clarify a bit more?

You are working with three components? DNA, an enzyme and a DNA intercalating molecule? 

You want to study complex stability? 

Dear Amali,

Generally the more hydrogen bonding you have the more the complex is stabilized. However, if you have two different systems it will be difficult to predict if the system with more hydrogen bonding is more stable than that of the two since there is another factor which should be considered which is the strength of the hydrogen bonding.

Generally if the hydrogen bonding is short and its torsion angle is close to linearity the bond will be strong and vice versa.

Therefore the factors to be considered:

1-Number of hydrogen bonding

2-The nature of the hydrogen bonding (the atoms involved in the bonding).

3-The length of the hydrogen bonding and its torsion angle.

Hoping this will be helpful,

Rafik

Considering H-bonding alone will not be sufficient to understand the ligand affinity because the DNA intercalation involves other forces - hydrophobic interactions, probably pi-stacking, and perhaps pi-cation interactions and electrostatic interactions if the ligand has a positive charge. The same potentially applies to the binding interaction with the protein.

Thank you everyone.. Yes I am working with 3 components.

1. DNA

2. Enzyme

3. Ligand

And I want to know how complex stability change when the ligand bind,

1. only with enzyme (with 3 polar interactions)

2. with enzyme (one polar interaction) and DNA (one polar interaction)